One aim of this blog was to advocate and advertise the use of open science. Which is somewhat at odds with my advocation and advertisement of Matlab – a popular, powerful, but ultimately pricey piece of software. I’ve spent some time working with Octave – a language that is identical in every way to Matlab, [...]... Read more »
The way by which living organisms in our planet are intricately connected is beautiful beyond comprehension. Like pieces in a puzzle they all fit together with the activities of each organism however trivial it may appear to be, affecting the existance of others. We will never fully understand this marvel, but a noteworthy example is the elegant finding by Lavery et al published in the Proceedings of the Royal Society (Biological Sciences)- Iron defecation by sperm whales stimulates carbon expo........ Read more »
Lavery, T., Roudnew, B., Gill, P., Seymour, J., Seuront, L., Johnson, G., Mitchell, J., & Smetacek, V. (2010) Iron defecation by sperm whales stimulates carbon export in the Southern Ocean. Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2010.0863
by Mary in OpenHelix
A couple of years back at a conference I was introduced to Biocatalogue. It seemed to me to be a really useful idea: locate bioinformatics tools and databases that are web-accessible, and that also have a mechanism to use the web service features to access the tool/server using strategies that don’t require the main web interface of the site. There are some introductions to the concept of web services out there–some of them are more for introduction, but most are aimed at prog........ Read more »
Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., Wolstencroft, K., Aleksejevs, S., Stevens, R., Pettifer, S.... (2010) BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Research. DOI: 10.1093/nar/gkq394
In studies, rodents generally prefer sugars over amino acids/proteins when given the choice, and this seems to reflect their ability to bind to the sweet T1R2/T1R3 receptor on the tongue. Postingestion, however, nutrients obviously differentially effect hormones involved in fuel mobilization (e.g. insulin and glucagon), so mechanisms should exist to influence appetite for specific macronutrients. [...]... Read more »
Ren, X., Ferreira, J., Zhou, L., Shammah-Lagnado, S., Yeckel, C., & de Araujo, I. (2010) Nutrient Selection in the Absence of Taste Receptor Signaling. Journal of Neuroscience, 30(23), 8012-8023. DOI: 10.1523/JNEUROSCI.5749-09.2010
... Read more »
Huckstorf, V., Lewin, W., Mehner, T., & Wolter, C. (2010) Impoverishment of YOY-fish assemblages by intense commercial navigation in a large Lowland river. River Research and Applications. DOI: 10.1002/rra.1420
As blogged before, overweight and obese patients frequently present with fibromyalgia, characterized by chronic pain, fatigue and depressed mood.
A paper by Akiko Okifuji from the University of Utah, Salt Lake City, just published in the Journal of Pain, examines the relationship between fibromyalgia and obesity in pain, function, mood, and sleep.
The study examines the impact [...]... Read more »
Okifuji A, Donaldson GW, Barck L, & Fine PG. (2010) Relationship Between Fibromyalgia and Obesity in Pain, Function, Mood, and Sleep. The journal of pain : official journal of the American Pain Society. PMID: 20542742
Dogs are particularly good at tasks that involve communicating or cooperating with humans, which has led some researchers to speculate that they are really good at solving social tasks, more generally. For example, dogs can figure out where a human's attention is, are really good at picking up on eye-gaze and finger pointing cues, distinguish among different individual humans (by contrast, humans are really bad at distinguishing among different individual monkeys, for example), and at least in o........ Read more »
Wobber, V., & Hare, B. (2009) Testing the social dog hypothesis: Are dogs also more skilled than chimpanzees in non-communicative social tasks?. Behavioural Processes, 81(3), 423-428. DOI: 10.1016/j.beproc.2009.04.003
A recent survey of over 4,000 UK employees conducted by GfK NOP found that one in four were planning to leave their organisation within the next year. The survey suggests these intentions are linked to the actions taken by the employers dealing with the effects of the recession. Continuing measures such as redundancies, recruitment freezes, [...]... Read more »
Brockner, J. (1992) Managing the effects of layoffs on survivors. California Management Review, 34(2), 9-28. info:/
Robinson, S., & Rousseau, D. (1994) Violating the psychological contract: Not the exception but the norm. Journal of Organizational Behavior, 15(3), 245-259. DOI: 10.1002/job.4030150306
Beugre, C., & Baron, R. (2001) Perceptions of systemic justice: The effects of distributive, procedural, and interactional justice. Journal of Applied Social Psychology, 31(2), 324-339. DOI: 10.1111/j.1559-1816.2001.tb00199.x
Brockner, J. (1995) Decision Frame, Procedural Justice, and Survivors′ Reactions to Job Layoffs. Organizational Behavior and Human Decision Processes, 63(1), 59-68. DOI: 10.1006/obhd.1995.1061
Children with Tourette's Syndrome, the neurodevelopmental condition characterised by involuntary motor and verbal tics, have superior timing abilities compared with their healthy age-matched peers, a new study suggests.Carmelo Vicario and colleagues tested nine children with Tourette's (average age 11 years) and 10 controls (average age 12) on timing perception and timing production. The former involved the children judging whether two circles were on screen for the same length of time or not. T........ Read more »
Vicario, C., Martino, D., Spata, F., Defazio, G., Giacchè, R., Martino, V., Rappo, G., Pepi, A., Silvestri, P., & Cardona, F. (2010) Time processing in children with Tourette’s syndrome. Brain and Cognition, 73(1), 28-34. DOI: 10.1016/j.bandc.2010.01.008
A while ago I wrote about the value of genome sequences, not just for helping us understand the biology of a particular organism, but also for enabling large-scale comparisons across species that can help spot patterns in genome evolution which wouldn’t otherwise be apparent. A recent paper in Journal of Heredity by Craig Lowe, David Haussler and [...]... Read more »
There’s a ubiquitous problem in experimental psychology studies that use behavioral measures that require participants to make speeded responses. The problem is that, in general, the longer people take to do something, the more likely they are to do it correctly. If I have you do a visual search task and ask you to tell [...]... Read more »
Yarkoni T, Barch DM, Gray JR, Conturo TE, & Braver TS. (2009) BOLD correlates of trial-by-trial reaction time variability in gray and white matter: a multi-study fMRI analysis. PloS one, 4(1). PMID: 19165335
Grinband J, Wager TD, Lindquist M, Ferrera VP, & Hirsch J. (2008) Detection of time-varying signals in event-related fMRI designs. NeuroImage, 43(3), 509-20. PMID: 18775784
Sci was incredibly excited to see this paper come out. It's got lots of stuff going for it, and all its powers combined were enough to send Sci bouncing around in her seat and sending emails to Ed Yong saying "OMG COOL PAPER!!".
What's it got, you say? It's got the meaning of life, the universe, and that pesky MRI signal.
Lee et al. "Global and local fMRI signals driven by neurons defined optogenetically by type and wiring" Nature, 2010.
Ah, the pretty brain picture. But what does it........ Read more »
Lee, J., Durand, R., Gradinaru, V., Zhang, F., Goshen, I., Kim, D., Fenno, L., Ramakrishnan, C., & Deisseroth, K. (2010) Global and local fMRI signals driven by neurons defined optogenetically by type and wiring. Nature, 465(7299), 788-792. DOI: 10.1038/nature09108
Last week I wrote about the potential impacts of caffeine (in coffee and energy drinks) on students and their study (here). In short, however, these were what I considered the most relevant findings: Keleman and Creeley (2001)found that Caffeine reliably improves hit rates for sustained attention, that there was an interaction between caffeine and free [...]... Read more »
Berto, R., Baroni, M., Zainaghi, A., & Bettella, S. (2009) An exploratory study of the effect of high and low fascination environments on attentional fatigue. Journal of Environmental Psychology. DOI: 10.1016/j.jenvp.2009.12.002
Kelemen WL, & Creeley CE. (2001) Caffeine (4 mg/kg) influences sustained attention and delayed free recall but not memory predictions. Human psychopharmacology, 16(4), 309-319. PMID: 12404566
Warburton DM, Bersellini E, & Sweeney E. (2001) An evaluation of a caffeinated taurine drink on mood, memory and information processing in healthy volunteers without caffeine abstinence. Psychopharmacology, 158(3), 322-8. PMID: 11713623
Oei A, & Hartley LR. (2005) The effects of caffeine and expectancy on attention and memory. Human psychopharmacology, 20(3), 193-202. PMID: 15742338
Yes, it would be great if we never spilled a drop of oil. No matter how hard we may try, though, the fact is that nobody is perfect, and oil spills are an inevitable consequence of our widespread use of oil. The question is, once the oil is out there, how do we clean it up? Perhaps my grandfather put it best, when I asked him what he thought about how BP and the US is responding to the spill.
"They're friggin' idiots."... Read more »
Jonathan L. Ramseur. (2010) Oil Spills in U.S. Coastal Waters: Background, Governance, and Issues for Congress. Congressional Research Service , 7-5700 (RL33705). info:/
Paine, R., Ruesink, J., Sun, A., Soulanille, E., Wonham, M., Harley, C., Brumbaugh, D., & Secord, D. (1996) TROUBLE ON OILED WATERS: Lessons from the Exxon Valdez Oil Spill. Annual Review of Ecology and Systematics, 27(1), 197-235. DOI: 10.1146/annurev.ecolsys.27.1.197
SWEDMARK, M., GRANMO, A., & KOLLBERG, S. (1973) Effects of oil dispersants and oil emulsions on marine animals. Water Research, 7(11), 1649-1672. DOI: 10.1016/0043-1354(73)90134-6
Oil is bad for wildlife. Period. But we really do not understand how it is bad. What does it do? Can marine organisms respond physiologically to oil in diets? For instance, translocate the toxic components to feathers and molt it off, much like some crabs, or have other physiologically mechanisms to . . . → Read More: Why Oil-Laden Prey is Bad for Sea Birds... Read more »
Pérez, C., Lores, M., & Velando, A. (2010) Oil pollution increases plasma antioxidants but reduces coloration in a seabird. Oecologia. DOI: 10.1007/s00442-010-1677-2
I’ve covered this sad state of affairs and one of Australia’s more notable biodiversity embarrassments over the last year (see Shocking continued loss of Australian mammals and Can we solve Australia’s mammal extinction crisis?), and now the most empirical demonstration of this is now published. The biodiversity guru of Australia’s tropical north, John Woinarksi, has [...]... Read more »
Woinarski, J., Armstrong, M., Brennan, K., Fisher, A., Griffiths, A., Hill, B., Milne, D., Palmer, C., Ward, S., Watson, M.... (2010) Monitoring indicates rapid and severe decline of native small mammals in Kakadu National Park, northern Australia. Wildlife Research, 37(2), 116. DOI: 10.1071/WR09125
The skull of Mosasaurus hoffmani. From Lingham-Soliar 1995.
On my first trip to the Inversand marl pit in Sewell, New Jersey, I didn't find the wonderfully preserved Dryptosaurus skeleton I had been dreaming of. I picked up a number of Cretaceous bivalve shells and Paleocene sponges, but other than a few scraps of "Chunkosaurus" my excavations didn't yield very much. Before my paleontology class left the site, though, we took a walk by the spoil piles - great green mounds of sediment that ha........ Read more »
KIERNAN, C. (2002) STRATIGRAPHIC DISTRIBUTION AND HABITAT SEGREGATION OF MOSASAURS IN THE UPPER CRETACEOUS OF WESTERN AND CENTRAL ALABAMA, WITH AN HISTORICAL REVIEW OF ALABAMA MOSASAUR DISCOVERIES. Journal of Vertebrate Paleontology, 22(1), 91-103. DOI: 10.1671/0272-4634(2002)022[0091:SDAHSO]2.0.CO;2
Lingham-Soliar, T. (1995) Anatomy and Functional Morphology of the Largest Marine Reptile Known, Mosasaurus hoffmanni (Mosasauridae, Reptilia) from the Upper Cretaceous, Upper Maastrichtian of the Netherlands. Philosophical Transactions of the Royal Society B: Biological Sciences, 347(1320), 155-172. DOI: 10.1098/rstb.1995.0019
Mulder, E. (1999) Transatlantic latest Cretaceous mosasaurs (Reptilia, Lacertilia) from the Maastrichtian type area and New Jersey. Geologie en Mijnbouw, 78(3/4), 281-300. DOI: 10.1023/A:1003838929257
Three months ago, I ran the post that appears below. This post got lots of comments, and there were a fair number of misunderstandings, so let me up-front here make clear what I mean by facilitated communication in the hopes these misunderstandings do not occur again. We teach our children many skills by using hand-over-hand techniques. I'm not talking about teaching your child how to type, how to hold a pencil, how to do things. I'm talking specifically about the facilitated communication as Bi........ Read more »
Finn, P. (2005) Science and Pseudoscience in Communication Disorders: Criteria and Applications. American Journal of Speech-Language Pathology, 14(3), 172-186. DOI: 10.1044/1058-0360(2005/018)
Wegner, D., Fuller, V., & Sparrow, B. (2003) Clever hands: Uncontrolled intelligence in facilitated communication. Journal of Personality and Social Psychology, 85(1), 5-19. DOI: 10.1037/0022-3518.104.22.168
Ziring, P., Brazdziunas, D., Cooley, W., Kastner, T., Kummer, M., De Pijem, L., & et al. (1998) Auditory integration training and facilitated communication for autism. American Academy of Pediatrics. Committee on Children with Disabilities. Pediatrics, 102(2 Pt 1), 431-3. PMID: 9685446
Our planet is an intriguing concoction of variables that meld together for successes spanning the organization of life (species, populations, communities, and ecosystems). It is literally an evolutionary process that is ecologically driven. And as a genotypic sex determined species, we seem to have an inherent fascination with the mysterious adaptive significance of environmental sex [...]... Read more »
HAYS, G., FOSSETTE, S., KATSELIDIS, K., SCHOFIELD, G., & GRAVENOR, M. (2010) Breeding Periodicity for Male Sea Turtles, Operational Sex Ratios, and Implications in the Face of Climate Change. Conservation Biology. DOI: 10.1111/j.1523-1739.2010.01531.x
Offering people free lentils and metal food dishes substantially improves the number of young children that receive a full course of childhood immunisations in resource poor areas, and is more cost effective than just improving the vaccine services available in the region, according to a new study published free in the British Medical Journal. Abhijit [...]... Read more »
Banerjee, A., Duflo, E., Glennerster, R., & Kothari, D. (2010) Improving immunisation coverage in rural India: clustered randomised controlled evaluation of immunisation campaigns with and without incentives. BMJ, 340(may17 1). DOI: 10.1136/bmj.c2220
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